I have wondered that myself. The argument she would have contacted somebody has some weight, but on the other hand, if she took him and ran because she felt like they were both in danger, she might well have tried to cover her tracks.
Though the news about Yellowstone Park has really shaken my belief that the kids are okay somewhere. That's not a place you can really run away from, y'know? Too isolated.
And if Tylee ran away from there then how she ends up with JJ is problematic. As far as that goes, even if we assume Tylee went home from Yellowstone and all was well I find it hard to swallow that Lori unenrolled JJ from school and Tylee then took off with him immediately after with no one seeing him since. I suppose Tylee could have taken off with him after he got out of school on 9/23 and Lori unenrolled him so no one would know anything was afoot, but that seems like a stretch too.